# Examples¶

## The Very Basics¶

```>>> import lingpy
>>> import lingpy as lp
```

```>>> from lingpy import *
```

## Alignment Analyses¶

Carry out a multiple alignment analysis of four sequences. First, define the sequences:

```>>> seqs = ['woldemort','waldemar','wladimir','vladymyr']
```

Create an instance of the `Multiple` class:

```>>> msa = Multiple(seqs)
```

Align the sequences, using simple progressive alignment with default parameters:

```>>> msa.prog_align()
```

Print out the results to the screen:

```>>> print(msa)
w    o    l    -    d    e    m    o    r    t
w    a    l    -    d    e    m    a    r    -
w    -    l    a    d    i    m    i    r    -
v    -    l    a    d    y    m    y    r    -
```

Use a short-cut to align the four sequences:

```>>> mult_align(['woldemort', 'waldemar', 'wladimir', 'vladymyr'], pprint=True)
```

## Reconstruction of Phylogenetic Trees¶

Import LingPy:

```>>> from lingpy import *
```

Import the squareform-function for convenience:

```>>> from lingpy.algorithm import squareform
```

Set up a couple of languages:

```>>> languages = ['Norwegian','Swedish','Icelandic','Dutch','English']
```

Define a distance matrix:

```>>> distances = squareform([0.5,0.67,0.8,0.2,0.4,0.7,0.6,0.8,0.8,0.3])
```

Carry out a Neighbor-Joining cluster analysis:

```>>> tree = neighbor(distances,languages)
>>> print(tree)
'(((Norwegian:0.18,(Swedish:0.12,Icelandic:0.28):0.21):0.17,Dutch:0.31):-0.01,English:-0.01);'
```

Print the tree in ASCII-Art to the screen (using PyCogent’s tree class):

```>>> tree = Tree(tree)
>>> print(tree.asciiArt())
/-Norwegian
/edge.1--|
|         |          /-Swedish
/edge.2--|          \edge.0--|
|         |                    \-Icelandic
-root----|         |
|          \-Dutch
|
\-English
```